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Hi Ralf,<br>
<br>
in fact, phenix.refine outputs information about refined f' and f'' in
ready-to-PDB-deposit format under RAMARK 3 prefix. For eample:<br>
<br>
REMARK 3 <br>
REMARK 3 ANOMALOUS SCATTERER GROUPS DETAILS.<br>
REMARK 3 NUMBER OF ANOMALOUS SCATTERER GROUPS : 2 <br>
REMARK 3 ANOMALOUS SCATTERER GROUP : 1 <br>
REMARK 3 SELECTION: name BR<br>
REMARK 3 fp : -0.8792 <br>
REMARK 3 fdp : 5.8029 <br>
REMARK 3 ANOMALOUS SCATTERER GROUP : 2 <br>
REMARK 3 SELECTION: name CO<br>
REMARK 3 fp : 0.0000 <br>
REMARK 3 fdp : 0.0000 <br>
REMARK 3 <br>
<br>
<br>
I hope this information is preserved when such structures get deposited
into PDB -:)<br>
<br>
Pavel.<br>
<br>
<br>
On 1/20/10 9:44 PM, Ralf W. Grosse-Kunstleve wrote:
<blockquote cite="mid:201001210544.o0L5i02J000459@cci.lbl.gov"
type="cite">
<blockquote type="cite">
<pre wrap="">Do I understand correctly that there is no way to force refine to skip
the serial in the output pdb file name, i.e. foo.pdb, not foo_001.pdb?
</pre>
</blockquote>
<pre wrap=""><!---->
Yes, that's true.
The main reason is that the same run writes
foo_001.eff
foo_002.def
When I implemented this I thought the serial numbers are the only
practical way to keep things straight.
Later we added storage of refined f' and f" to the .def file (since
there is no place in the .pdb file that would survive passes through
external programs). Because of this the serial numbers seem even more
important to me.
Ralf
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</pre>
</blockquote>
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